So I got this HP iPAQ 3600 second hand from a friend. When I plugged it in and turned it on i got a boot error message telling me that it had an ivalid OS. Now does anyone know how to put a new OS on to a Pocket PC and if it can even be done?

That could be possible if the ROM is corrupted due to an incorrect flash upgrade. Did you try hard reset the device? If it still happens, look for a valid ROM, and you'll need to flash it in hopes it erases the problem.